ProCogGraph: a graph-based mapping of cognate ligand domain interactions.

ABSTRACT:

Motivation

Mappings of domain-cognate ligand interactions can enhance our understanding of the core concepts of evolution and be used to aid docking and protein design. Since the last available cognate-ligand domain database was released, the PDB has grown significantly and new tools are available for measuring similarity and determining contacts.

Results

We present ProCogGraph, a graph database of cognate-ligand domain mappings in PDB structures. Building upon the work of the predecessor database, PROCOGNATE, we use data-driven approaches to develop thresholds and interaction modes. We explore new aspects of domain-cognate ligand interactions, including the chemical similarity of bound cognate ligands and how domain combinations influence cognate ligand binding. Finally, we

SUBMITTER: Crown M 

PROVIDER: S-EPMC11561043 | biostudies-literature | 2024

REPOSITORIES: biostudies-literature